PLVAP

plasmalemma vesicle associated protein

Basic information

Region (hg38): 19:17351450-17377342

Links

ENSG00000130300 ∙ NCBI:83483 ∙ OMIM:607647 ∙ HGNC:13635 ∙ Uniprot:Q9BX97 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• diarrhea 10, protein-losing enteropathy type (Strong), mode of inheritance: AR
• diarrhea 10, protein-losing enteropathy type (Moderate), mode of inheritance: AR
• diarrhea 10, protein-losing enteropathy type (Strong), mode of inheritance: AR
• congenital diarrhea 7 with exudative enteropathy (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Diarrhea 10, protein-losing enteropathy type	AR	Gastrointestinal	The condition can involve severe protein-losing enteropathy, and awareness may allow early diagnosis and management (eg, with low-fat diet and middle-chain triglyceride-rich formula) which has been reported as beneficial in some individuals	Craniofacial; Gastrointestinal; Genitourinary	26207260; 29661969; 29875123

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLVAP gene.

• not provided (2 variants)
• Diarrhea 10, protein-losing enteropathy type (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLVAP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				54	7	61
missense			76	13	4	93
nonsense	2					2
start loss						0
frameshift	1	2				3
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region			3	8		11
non coding				9	2	11
Total	3	2	77	76	13

Highest pathogenic variant AF is 0.0000197

Variants in PLVAP

This is a list of pathogenic ClinVar variants found in the PLVAP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
19-17352374-G-A			Likely benign (Oct 02, 2022)
19-17352376-A-G			Likely benign (Sep 27, 2023)
19-17360517-C-T			Likely benign (Nov 07, 2023)
19-17360521-G-A			Likely benign (Dec 09, 2023)
19-17360537-G-A		PLVAP-related disorder	Benign (Dec 11, 2023)
19-17360542-A-G			Likely benign (Oct 07, 2022)
19-17360554-A-G		PLVAP-related disorder	Benign (Jan 31, 2024)
19-17360556-G-A		PLVAP-related disorder	Uncertain significance (Apr 16, 2022)
19-17360572-C-T			Likely benign (Jun 26, 2022)
19-17360576-A-G			Uncertain significance (Aug 06, 2022)
19-17360581-C-T			Likely benign (Mar 14, 2022)
19-17360590-C-T			Likely benign (Aug 19, 2022)
19-17360625-G-C			Likely benign (Dec 03, 2022)
19-17360628-G-A			Likely benign (Jan 13, 2024)
19-17360762-T-C			Likely benign (Jan 07, 2024)
19-17360773-G-A			Uncertain significance (Mar 13, 2022)
19-17360778-G-A			Uncertain significance (Jun 22, 2022)
19-17360779-C-G			Uncertain significance (Aug 10, 2022)
19-17360779-C-T			Likely benign (Sep 17, 2022)
19-17360782-G-C			Benign (Feb 27, 2023)
19-17360784-G-T		Inborn genetic diseases	Uncertain significance (Aug 08, 2022)
19-17360797-G-A			Likely benign (Jan 20, 2024)
19-17360815-T-G			Likely benign (Jul 17, 2023)
19-17360821-C-T		Inborn genetic diseases	Likely benign (Oct 29, 2021)
19-17360824-C-T			Likely benign (Nov 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLVAP	protein_coding	protein_coding	ENST00000252590	6	25903

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000230	0.911	125724	0	23	125747	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.549	267	293	0.910	0.0000195	2900
Missense in Polyphen		95	109.39	0.86843		1094
Synonymous	-0.984	133	119	1.11	0.00000762	872
Loss of Function	1.66	12	20.0	0.600	0.00000104	213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000173	0.000173
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the formation of stomatal and fenestral diaphragms of caveolae. May function in microvascular permeability. {ECO:0000269|PubMed:15155804}.

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: -0.57
• rvis_percentile_EVS: 18.9

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.210
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.328

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Plvap
• Phenotype: respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); digestive/alimentary phenotype; limbs/digits/tail phenotype; renal/urinary system phenotype; homeostasis/metabolism phenotype; immune system phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: MAPK cascade;positive regulation of cellular extravasation;tumor necrosis factor-mediated signaling pathway;protein kinase C signaling
• Cellular component: caveola;cell surface;integral component of membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding;protein homodimerization activity